Numerically simulating an infinite domain foundation is an important method for solving structural dynamics problems. This paper introduces several artificial dynamic boundaries commonly used in the study of structural dynamics, and elaborates the theory and methods of the dynamic infinite element method boundary (IEMB) and viscous–spring artificial boundary (VSAB). The capacity of different boundary effects on seismic waves energy absorption is verified by establishing a layered half-space model. An irrigation aqueduct is taken as a research object. The IEMB, VSAB, and fixed boundary (FB) models are established and the Concrete Damaged Plasticity (CDP) constitutive is introduced, which is aimed at studying the dynamic failure mechanism and the rules of damage development to the aqueduct structure during the seismic duration. The results for the IEMB and VSAB show better energy absorption for the incident waves and a better simulation result for the damping effect of the far field foundation than that of the FB. Comparing the maximum displacement response rules of the three boundaries, it is seen that the maximum displacement response values of the VSAB and dynamic IEMB increased by 6%–48% and 9%–35%, respectively, over the FB. The calculation results of the VSAB are similar to that of the IEMB. The difference between the maximum acceleration response values is 2%–17% whereas the difference between the maximum displacement response values is 0.4%–19%. The IEMB studied in this paper provides a theoretical reference for large–scale building boundary treatment in structural dynamics calculations.